Avoid using pydicom 3 (for now), as it seems to cause random test fai…

…lures

bidscoin/bids.py

@@ -1284,7 +1284,7 @@ def get_matching_run(self, datasource: DataSource, runtime=False) -> Tuple[RunIt
 
         unknowndatatypes = self.options.get('unknowntypes') or ['unknown_data']
         ignoredatatypes  = self.options.get('ignoretypes') or []
-        bidsdatatypes    = sorted([dtype.datatype for dtype in self.dataformat(datasource.dataformat).datatypes if dtype not in unknowndatatypes + ignoredatatypes])
+        bidsdatatypes    = [dtype.datatype for dtype in self.dataformat(datasource.dataformat).datatypes if dtype not in unknowndatatypes + ignoredatatypes]
         datasource       = copy.deepcopy(datasource)
         rundata          = {'provenance': str(datasource.path), 'properties': {}, 'attributes': {}, 'bids': {}, 'meta': {}}
         """The a run-item data structure. NB: Keep in sync with the RunItem() data attributes"""
@@ -1457,6 +1457,13 @@ def delete_run(self, provenance: Union[RunItem, str], datatype: Union[str, DataT
         dtype   = dformat.datatype(str(datatype) or runitem.datatype)
         dtype.delete_run(provenance)
 
+    def delete_runs(self):
+        """Delete all run-items from the bidsmap"""
+
+        for dataformat in self.dataformats:
+            for datatype in dataformat.datatypes:
+                dataformat.delete_runs(datatype)
+
     def insert_run(self, runitem: RunItem, position: int=None):
         """
         Inserts a run-item (as is) to the BIDS map (e.g. allowing you to insert a run-item from another bidsmap).

bidscoin/bidseditor.py

@@ -93,9 +93,7 @@ def __init__(self, bidsfolder: Path, input_bidsmap: BidsMap, template_bidsmap: B
                     template_bidsmap.plugins = input_bidsmap.plugins    # Always use the plugins of the input bidsmap
             else:
                 input_bidsmap = copy.deepcopy(template_bidsmap)
-                for dataformat in input_bidsmap.dataformats:
-                    for datatype in dataformat.datatypes:
-                        dataformat.delete_runs(datatype)
+                input_bidsmap.delete_runs()
 
         # Keep track of the EditWindow status
         self.editwindow_opened: Union[str,None] = None

bidscoin/bidsmapper.py

@@ -89,9 +89,7 @@ def bidsmapper(sourcefolder: str, bidsfolder: str, bidsmap: str, template: str,
         bidsmap_new.options['unzip'] = unzip
     else:
         unzip = bidsmap_new.options.get('unzip','')
-    for dataformat in bidsmap_new.dataformats:
-        for datatype in dataformat.datatypes:
-            dataformat.delete_runs(datatype)
+    bidsmap_new.delete_runs()
 
     # Store/retrieve the empty or user-defined sub-/ses-prefix. The new bidsmap is now ready to be populated
     subprefix, sesprefix = setprefix(bidsmap_new, subprefix, sesprefix, rawfolder, update = not no_update)

pyproject.toml

@@ -20,7 +20,7 @@ classifiers      = ['Programming Language :: Python :: 3.8',
 dependencies     = ['pandas',
                     'matplotlib',
                     'numpy',
-                    'pydicom >= 2',
+                    'pydicom >= 2, < 3',
                     'PyQt6',
                     'ruamel-yaml > 0.17.2',
                     'tomli >= 1.1.0 ; python_version < "3.11"',